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- PDB-6bzf: Structure of S. cerevisiae Zip2:Spo16 complex, C2 form -

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Basic information

Entry
Database: PDB / ID: 6bzf
TitleStructure of S. cerevisiae Zip2:Spo16 complex, C2 form
Components
  • (Protein ZIP2) x 3
  • (Sporulation-specific protein ...) x 2
KeywordsDNA BINDING PROTEIN / XPF-ERCC1 Meiosis Recombination
Function / homology
Function and homology information


regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination ...regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination / reciprocal meiotic recombination / nuclear chromosome / protein sumoylation / condensed nuclear chromosome / nucleotide binding / mitochondrion
Similarity search - Function
Spo16 protein / : / Spo16 protein, N-terminal / Spo16 protein, C-terminal
Similarity search - Domain/homology
Sporulation-specific protein 16 / Protein ZIP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.286 Å
AuthorsArora, K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104141 United States
Citation
Journal: Nucleic Acids Res. / Year: 2019
Title: The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding.
Authors: Arora, K. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2018
Title: Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation
Authors: Arora, K. / Corbett, K.D.
History
DepositionDec 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sporulation-specific protein 16
B: Protein ZIP2
C: Sporulation-specific protein 16
D: Protein ZIP2
E: Sporulation-specific protein 16
F: Protein ZIP2
G: Sporulation-specific protein 16
H: Protein ZIP2


Theoretical massNumber of molelcules
Total (without water)199,9648
Polymers199,9648
Non-polymers00
Water4,035224
1
A: Sporulation-specific protein 16
B: Protein ZIP2


Theoretical massNumber of molelcules
Total (without water)50,0112
Polymers50,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-37 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: Sporulation-specific protein 16
D: Protein ZIP2


Theoretical massNumber of molelcules
Total (without water)50,0112
Polymers50,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-38 kcal/mol
Surface area20170 Å2
MethodPISA
3
E: Sporulation-specific protein 16
F: Protein ZIP2


Theoretical massNumber of molelcules
Total (without water)49,9842
Polymers49,9842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-35 kcal/mol
Surface area19530 Å2
MethodPISA
4
G: Sporulation-specific protein 16
H: Protein ZIP2


Theoretical massNumber of molelcules
Total (without water)49,9572
Polymers49,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-33 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.402, 63.589, 199.043
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Sporulation-specific protein ... , 2 types, 4 molecules AECG

#1: Protein Sporulation-specific protein 16


Mass: 25380.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122
#3: Protein Sporulation-specific protein 16


Mass: 25353.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122

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Protein , 3 types, 4 molecules BDFH

#2: Protein Protein ZIP2 / Zipping up meiotic chromosomes protein 2


Mass: 24630.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061
#4: Protein Protein ZIP2 / Zipping up meiotic chromosomes protein 2


Mass: 24657.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061
#5: Protein Protein ZIP2 / Zipping up meiotic chromosomes protein 2


Mass: 24603.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061

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Non-polymers , 1 types, 224 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.6 / Details: 1.4 M Na-K phosphate pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.286→100 Å / Num. obs: 95052 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rsym value: 0.091 / Net I/σ(I): 11.1
Reflection shellResolution: 2.286→2.33 Å / Num. unique obs: 10085 / CC1/2: 0.328 / Rsym value: 1.08

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZG

6bzg


Resolution: 2.286→57.093 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.41
RfactorNum. reflection% reflection
Rfree0.2498 4806 5.07 %
Rwork0.1956 --
obs0.1984 94878 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.286→57.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12957 0 0 224 13181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813201
X-RAY DIFFRACTIONf_angle_d0.87317823
X-RAY DIFFRACTIONf_dihedral_angle_d14.6497900
X-RAY DIFFRACTIONf_chiral_restr0.0512027
X-RAY DIFFRACTIONf_plane_restr0.0042240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.286-2.3120.39541400.36492670X-RAY DIFFRACTION88
2.312-2.33920.39071560.34932966X-RAY DIFFRACTION98
2.3392-2.36770.37891730.31633010X-RAY DIFFRACTION99
2.3677-2.39770.34211620.29232992X-RAY DIFFRACTION100
2.3977-2.42920.33651450.27013074X-RAY DIFFRACTION100
2.4292-2.46250.32611330.2673036X-RAY DIFFRACTION100
2.4625-2.49770.28961720.25913023X-RAY DIFFRACTION100
2.4977-2.53490.31681830.25082999X-RAY DIFFRACTION100
2.5349-2.57460.30791440.24463048X-RAY DIFFRACTION100
2.5746-2.61680.30811410.2433022X-RAY DIFFRACTION100
2.6168-2.66190.31641730.23483059X-RAY DIFFRACTION99
2.6619-2.71030.31741590.24222943X-RAY DIFFRACTION99
2.7103-2.76240.29991610.2393071X-RAY DIFFRACTION100
2.7624-2.81880.29941780.2433000X-RAY DIFFRACTION100
2.8188-2.88010.31031830.24093008X-RAY DIFFRACTION100
2.8801-2.94710.30051550.24323023X-RAY DIFFRACTION100
2.9471-3.02080.27841740.22493074X-RAY DIFFRACTION100
3.0208-3.10250.30551470.21643005X-RAY DIFFRACTION99
3.1025-3.19370.27141540.20543062X-RAY DIFFRACTION99
3.1937-3.29680.26811790.20282951X-RAY DIFFRACTION99
3.2968-3.41460.22651290.18653059X-RAY DIFFRACTION99
3.4146-3.55130.23211560.17792978X-RAY DIFFRACTION97
3.5513-3.71290.22971520.17522970X-RAY DIFFRACTION97
3.7129-3.90860.23221620.16592959X-RAY DIFFRACTION97
3.9086-4.15350.19371660.14892982X-RAY DIFFRACTION98
4.1535-4.4740.18091380.13753015X-RAY DIFFRACTION97
4.474-4.92410.19111720.13782997X-RAY DIFFRACTION97
4.9241-5.6360.21491910.16512998X-RAY DIFFRACTION98
5.636-7.09870.24521670.1983010X-RAY DIFFRACTION97
7.0987-57.11130.19791610.17323068X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.29580.7719-0.28532.0797-0.42350.6868-0.0244-0.08280.01560.0095-0.003-0.058-0.11380.0130.02890.26680.04490.02440.3527-0.01790.2684-3.307120.795365.1428
20.9075-0.6416-0.1351.81580.59140.67680.00040.0556-0.0996-0.1003-0.1040.1655-0.0705-0.0310.10430.2786-0.01690.00840.3846-0.01330.309-2.0942-10.974229.9811
31.04390.0785-0.51821.0952-0.32691.97420.04480.0515-0.11040.03770.00750.2161-0.0328-0.1102-0.0560.2390.0071-0.00140.24810.0020.410133.991123.468185.2844
41.24280.2839-0.67560.68140.06141.98110.0083-0.1226-0.1830.0279-0.041-0.03760.1370.05820.05490.23020.0576-0.02750.28680.00150.329247.322623.556315.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B
2X-RAY DIFFRACTION2chain C or chain D
3X-RAY DIFFRACTION3chain E or chain F
4X-RAY DIFFRACTION4chain G or chain H

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